Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans

Abstract

Tomato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are associated with migration of new and more aggressive populations of P. infestans in the field. The objective of this study was to reassess late blight resistance in the wild tomato accession L3708 (Solanum pimpinellifolium L.) against pathogens of different aggressiveness. An F2:3 genetic mapping population was developed using L3708 as the paternal parent. Two isolates of P. infestans, Pi39A and Pi733, were used for inoculation. Pi733 is a highly aggressive genotype that defeats three known late blight resistance genes, Ph-1, Ph-2, and Ph-5t in tomato. In contrast, Pi39A is a less aggressive genotype that defeats only Ph-1. Restriction site Associated DNA Sequencing (RAD-Seq) technology was used to massively sequence 90 bp nucleotides adjacent to both sides of PstI restriction enzyme cutting sites in the genome for all individuals in the genetic mapping population. The RAD-seq data were used to construct a genetic linkage map containing 440 single nucleotide polymorphism markers. Quantitative trait locus (QTL) analysis identified a new disease-resistant QTL specific to Pi733 on chromosome 2. The Ph-3 gene located on chromosome 9 could be detected whichever isolates were used. This study demonstrated the feasibility and efficiency of RAD-Seq technology for conducting a QTL mapping experiment using an F2:3 mapping population, which allowed the identification of a new late blight resistant QTL in tomato.

Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

“…The current number of SNPs is also much lower than discovered by Causse et al [16] (16,000 SNPs) and Kim et al [17] (4,680,647); however, these SNPs were not validated. The average frequency of SNPs identified in this study was 1 SNP per 256.4 kb, much higher than reported for the S. lycopersicum  ×  S. pimpinellifolium linkage maps of Salinan et al [13] (1 SNP per 8,482 kb), Capel et al [14] (1 SNP per 4,077 kb) and Chen et al [15] (1 SNP per 1,821 kb). Thus, the present research demonstrated that the GBS approach was efficient in constructing a SNP-based physical map of sufficient resolution for QTL mapping in tomato.…”

“…Nevertheless, a sufficient number of validated SNP markers (3,125 SNPs) remained and were found to be useful for QTL mapping. In comparison with previous work, this study discovered fewer validated SNPs than are available in The Solanaceae Genomics Network database (9,226 SNPs) and those reported by Chen et al [15] (4,697 SNPs). The current number of SNPs is also much lower than discovered by Causse et al [16] (16,000 SNPs) and Kim et al [17] (4,680,647); however, these SNPs were not validated.…”

“…The maps introduced by Salinan et al [13] and Capel et al [14], respectively, contained 112 and 233 SNP markers genotyped in S. pimpinellifolium and S. lycopersicum using the high-resolution melting (HRM) method. Another map with 440 markers was constructed with SNPs discovered by Restriction site Associated DNA Sequencing (RAD-Seq) technology and VeraCode SNP makers [15]. The TraitGenetics EXPIMP2012 linkage map had the highest number of interspecific SNP markers (4,491 SNPs) [12].…”

“…To date, the GBS approach has been commonly used for SNP discovery and genotyping in crop species such as wheat [21], rice [22] and maize [23]. However, the RAD-Seq method, which is similar to GBS has been used in tomato [15]. This technique was used to discover 4697 SNPs in an F2:3 population derived from a cross between S. pimpinellifolium (L3708) and S. lycopersicum (T3224) to identify QTLs for late blight resistance [15, 18]).…”

“…However, the RAD-Seq method, which is similar to GBS has been used in tomato [15]. This technique was used to discover 4697 SNPs in an F2:3 population derived from a cross between S. pimpinellifolium (L3708) and S. lycopersicum (T3224) to identify QTLs for late blight resistance [15, 18]). The primary goal of the current study was to use the GBS approach for high-throughput identification of interspecific SNPs in the S. pimpinellifolium (LA1589) and S. lycopersicum cv.…”